guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 108182dbb589e83de4ab46dd17b89860cef021cb
Author: Simon Tournier <[email protected]>
AuthorDate: Thu Jan 8 16:36:16 2026 +0100
gnu: velvet: Adjust for GCC@14 and documentation building.
* gnu/packages/bioinformatics.scm (velvet)
[arguments]:<make-flags>: Add incompatible-pointer-types.
<phases>: Allow TeXlive to create font.
[native-inputs]: Add texlive-ec.
Fixes: guix/guix#5471
Change-Id: I0d44b763a77a64c900f09efdea30d8a89d3b2496
Signed-off-by: Andreas Enge <[email protected]>
---
gnu/packages/bioinformatics.scm | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d063c276e0..194e5b9fd6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21143,7 +21143,8 @@ to an artifact/contaminant file.")
(build-system gnu-build-system)
(arguments
(list
- #:make-flags #~(list "OPENMP=t")
+ #:make-flags #~(list "OPENMP=t"
+ "CFLAGS=-Wall
-Wno-error=incompatible-pointer-types")
#:test-target "test"
#:phases
#~(modify-phases %standard-phases
@@ -21152,6 +21153,11 @@ to an artifact/contaminant file.")
(lambda _
(substitute* "src/binarySequences.c"
(("../third-party/zlib-1.2.3/zlib.h") "zlib.h"))))
+ (add-before 'build 'set-home-env
+ (lambda _
+ ;; TeXLive requires HOME to be set.
+ ;; Permission denied: '/homeless-shelter'
+ (setenv "HOME" "/tmp")))
(replace 'install
(lambda _
(let ((bin (string-append #$output "/bin"))
@@ -21166,7 +21172,8 @@ to an artifact/contaminant file.")
(list openmpi zlib))
(native-inputs
(list (texlive-local-tree
- (list texlive-infwarerr
+ (list texlive-ec
+ texlive-infwarerr
texlive-kvoptions
texlive-pdftexcmds))))
(home-page "https://www.ebi.ac.uk/~zerbino/velvet/";)
